X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=lefsecommand.cpp;h=e894d5781346802cc5250f0fb956a9d853b0017e;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=455019b4e456d7996ee2471eabf28a08f96ac87c;hpb=ad4f75fd7c938090d3b1ce4cfefcc21edf1869eb;p=mothur.git diff --git a/lefsecommand.cpp b/lefsecommand.cpp index 455019b..e894d57 100644 --- a/lefsecommand.cpp +++ b/lefsecommand.cpp @@ -7,3 +7,483 @@ // #include "lefsecommand.h" +#include "linearalgebra.h" + +//********************************************************************************************************************** +vector LefseCommand::setParameters(){ + try { + CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared); + CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass); + CommandParameter psubclass("subclass", "String", "", "", "", "", "","",false,false); parameters.push_back(psubclass); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pclasses("classes", "String", "", "", "", "", "","",false,false); parameters.push_back(pclasses); + CommandParameter palpha("anova_alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha); + CommandParameter pwalpha("wilcoxon_alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pwalpha); + //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files. + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string LefseCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The lefse command allows you to ....\n"; + helpString += "The lefse command parameters are: shared, design, class, subclass, label, classes, wilcoxon_alpha, anova_alpha.\n"; + helpString += "The class parameter is used to indicate the which category you would like used for the Kruskal Wallis analysis. If none is provided first category is used.\n"; + helpString += "The subclass parameter is used to indicate the .....If none is provided second category is used, or if only one category subclass is ignored. \n"; + helpString += "The classes parameter is used to indicate the classes you would like to use. Clases should be inputted in the following format: classes=label-label. For example to include groups from treatment with value early or late and age= young or old. class=treatment-age.\n"; + helpString += "The label parameter is used to indicate which distances in the shared file you would like to use. labels are separated by dashes.\n"; + helpString += "The lefse command should be in the following format: lefse(shared=final.an.shared, design=final.design, class=treatment, subclass=age).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string LefseCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],[distance],lefse_summary"; } + else if (type == "kruskall-wallis") { pattern = "[filename],[distance],kruskall_wallis"; } + else if (type == "wilcoxon") { pattern = "[filename],[distance],wilcoxon"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +LefseCommand::LefseCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + outputTypes["kruskall-wallis"] = tempOutNames; + outputTypes["wilcoxon"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "LefseCommand"); + exit(1); + } +} +//********************************************************************************************************************** +LefseCommand::LefseCommand(string option) { + try { + abort = false; calledHelp = false; + allLines = 1; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + //valid paramters for this command + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + outputTypes["kruskall-wallis"] = tempOutNames; + outputTypes["wilcoxon"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + + string path; + it = parameters.find("design"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["desing"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } + } + + //get shared file, it is required + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setSharedFile(sharedfile); } + + //get shared file, it is required + designfile = validParameter.validFile(parameters, "design", true); + if (designfile == "not open") { designfile = ""; abort = true; } + else if (designfile == "not found") { + //if there is a current shared file, use it + designfile = m->getDesignFile(); + if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setDesignFile(designfile); } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = m->hasPath(sharedfile); //if user entered a file with a path then preserve it + } + + string label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + mclass = validParameter.validFile(parameters, "class", false); + if (mclass == "not found") { mclass = ""; } + + subclass = validParameter.validFile(parameters, "subclass", false); + if (subclass == "not found") { subclass = ""; } + + classes = validParameter.validFile(parameters, "classes", false); + if (classes == "not found") { classes = ""; } + + string temp = validParameter.validFile(parameters, "anova_alpha", false); + if (temp == "not found") { temp = "0.05"; } + m->mothurConvert(temp, anovaAlpha); + + temp = validParameter.validFile(parameters, "wilcoxon_alpha", false); + if (temp == "not found") { temp = "0.05"; } + m->mothurConvert(temp, wilcoxonAlpha); + + } + + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "LefseCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int LefseCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + DesignMap designMap(designfile); + //if user set classes set groups=those classes + if (classes != "") { + map > thisClasses = m->parseClasses(classes); + vector groups = designMap.getNamesUnique(thisClasses); + if (groups.size() != 0) { m->setGroups(groups); } + else { m->mothurOut("[ERROR]: no groups meet your classes requirement, quitting.\n"); return 0; } + } + + //if user did not select class use first column + if (mclass == "") { mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); } + + InputData input(sharedfile, "sharedfile"); + vector lookup = input.getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + process(lookup, designMap); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(lastLabel); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + process(lookup, designMap); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + + if (m->control_pressed) { return 0; } + + //get next line to process + lookup = input.getSharedRAbundVectors(); + } + + if (m->control_pressed) { return 0; } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input.getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup, designMap); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + + + //output files created by command + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + return 0; + + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** + +int LefseCommand::process(vector& lookup, DesignMap& designMap) { + try { + //run kruskal wallis on each otu + vector significantOtuLabels = runKruskalWallis(lookup, designMap); + + //check for subclass + if (subclass != "") { significantOtuLabels = runWilcoxon(lookup, designMap, significantOtuLabels); } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "process"); + exit(1); + } +} +//********************************************************************************************************************** + +vector LefseCommand::runKruskalWallis(vector& lookup, DesignMap& designMap) { + try { + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[distance]"] = lookup[0]->getLabel(); + string outputFileName = getOutputFileName("kruskall-wallis",variables); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName); + out << "OTULabel\tKW\tPvalue\n"; + + vector significantOtuLabels; + int numBins = lookup[0]->getNumBins(); + //sanity check to make sure each treatment has a group in the shared file + set treatments; + for (int j = 0; j < lookup.size(); j++) { + string group = lookup[j]->getGroup(); + string treatment = designMap.get(group, mclass); //get value for this group in this category + treatments.insert(treatment); + } + if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things to classes to compare, quitting.\n"); m->control_pressed = true; } + + LinearAlgebra linear; + for (int i = 0; i < numBins; i++) { + if (m->control_pressed) { break; } + + vector values; + for (int j = 0; j < lookup.size(); j++) { + string group = lookup[j]->getGroup(); + string treatment = designMap.get(group, mclass); //get value for this group in this category + spearmanRank temp(treatment, lookup[j]->getAbundance(i)); + values.push_back(temp); + } + + double pValue = 0.0; + double H = linear.calcKruskalWallis(values, pValue); + + //output H and signifigance + out << m->currentBinLabels[i] << '\t' << H << '\t' << pValue << endl; + + if (pValue < anovaAlpha) { significantOtuLabels.push_back(i); } + } + out.close(); + + return significantOtuLabels; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "runKruskalWallis"); + exit(1); + } +} +//********************************************************************************************************************** + +vector LefseCommand::runWilcoxon(vector& lookup, DesignMap& designMap, vector bins) { + try { + vector significantOtuLabels; + //if it exists and meets the following requirements run Wilcoxon + /* + 1. Subclass members all belong to same main class + 2. Number of groups in each subclass is the same + 3. anything else?? + + */ + vector subclasses; + map subclass2Class; + map subclassCounts; + map > subClass2GroupIndex; //maps subclass name to vector of indexes in lookup from that subclass. old -> 1,2,3 means groups in location 1,2,3 of lookup are from old. Saves time below. + bool error = false; + for (int j = 0; j < lookup.size(); j++) { + string group = lookup[j]->getGroup(); + string treatment = designMap.get(group, mclass); //get value for this group in this category + string thisSub = designMap.get(group, subclass); + map::iterator it = subclass2Class.find(thisSub); + if (it == subclass2Class.end()) { + subclass2Class[thisSub] = treatment; + subclassCounts[thisSub] = 1; + vector temp; temp.push_back(j); + subClass2GroupIndex[thisSub] = temp; + } + else { + subclassCounts[thisSub]++; + subClass2GroupIndex[thisSub].push_back(j); + if (it->second != treatment) { + error = true; + m->mothurOut("[ERROR]: subclass " + thisSub + " has members in " + it->second + " and " + treatment + ". Subclass members must be from the same class. Ignoring wilcoxon.\n"); + } + } + } + + if (error) { return significantOtuLabels; } + else { //check counts to make sure subclasses are the same size + set counts; + for (map::iterator it = subclassCounts.begin(); it != subclassCounts.end(); it++) { counts.insert(it->second); } + if (counts.size() > 1) { m->mothurOut("[ERROR]: subclasses must be the same size. Ignoring wilcoxon.\n"); + return significantOtuLabels; } + } + + int numBins = lookup[0]->getNumBins(); + vector comp; + //find comparisons and fill comp + map::iterator itB; + for(map::iterator it=subclassCounts.begin();it!=subclassCounts.end();it++){ + itB = it;itB++; + for(itB;itB!=subclassCounts.end();itB++){ + compGroup temp(it->first,itB->first); + comp.push_back(temp); + } + } + + int numComp = comp.size(); + if (numComp < 2) { m->mothurOut("[ERROR]: Need at least 2 subclasses, Ignoring Wilcoxon.\n"); + return significantOtuLabels; } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[distance]"] = lookup[0]->getLabel(); + string outputFileName = getOutputFileName("wilcoxon",variables); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputNames.push_back(outputFileName); outputTypes["wilcoxon"].push_back(outputFileName); + out << "OTULabel\tComparision\tWilcoxon\tPvalue\n"; + + LinearAlgebra linear; + for (int i = 0; i < numBins; i++) { + if (m->control_pressed) { break; } + + if (m->inUsersGroups(i, bins)) { //flagged in Kruskal Wallis + + bool sig = false; + //for each subclass comparision + for (int j = 0; j < numComp; j++) { + //fill x and y with this comparisons data + vector x; vector y; + + //fill x and y + vector xIndexes = subClass2GroupIndex[comp[j].group1]; //indexes in lookup for this subclass + for (int k = 0; k < xIndexes.size(); k++) { x.push_back(lookup[xIndexes[k]]->getAbundance(i)); } + + vector yIndexes = subClass2GroupIndex[comp[j].group2]; //indexes in lookup for this subclass + for (int k = 0; k < yIndexes.size(); k++) { y.push_back(lookup[yIndexes[k]]->getAbundance(i)); } + + double pValue = 0.0; + double H = linear.calcWilcoxon(x, y, pValue); + + //output H and signifigance + out << m->currentBinLabels[i] << '\t' << comp[j].getCombo() << '\t' << H << '\t' << pValue << endl; + + //set sig - not sure how yet + } + if (sig) { significantOtuLabels.push_back(i); } + } + } + out.close(); + + return significantOtuLabels; + } + catch(exception& e) { + m->errorOut(e, "LefseCommand", "runWilcoxon"); + exit(1); + } +} + +//********************************************************************************************************************** + +